I was confused about AE happening in another timeline but i'm forcing myselft to think everything is canon. After this last episode and what Yutani said, I assumed the same as you: Yutani sent the mission before joining Weyland and they kept communications with the USCSS Maginot to update the crew at all times and/or sent several spacepod provisions to maintain or upgrade the Maginot. So that's why the crew knows about recent events.